Installing tools with the checkbox for "manage dependencies" will likely solve this. Uninstalling then reinstalling is often the best way rather than installing each dependency individually, but that is also possible if needed (some tools do not have all dependencies set up for this function).

Before doing this, make sure the value in your config/galaxy.ini file for tool_dependency_dir is set to an existing directory that Galaxy can write to.

# Path to the directory in which tool dependencies are placed. This is used by
# the tool shed to install dependencies and can also be used by administrators
# to manually install or link to dependencies. For details, see:
# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
# If this option is not set to a valid path, installing tools with dependencies
# from the Tool Shed will fail.
#tool_dependency_dir = None